# -*- coding: utf-8 -*- # Copyright 2007-2023 The HyperSpy developers # # This file is part of RosettaSciIO. # # RosettaSciIO is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # RosettaSciIO is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with RosettaSciIO. If not, see . import os import tempfile import zipfile from pathlib import Path import numpy as np import pytest from packaging.version import Version tifffile = pytest.importorskip("tifffile", reason="tifffile not installed") hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed") t = pytest.importorskip("traits.api", reason="traits not installed") import rsciio.tiff # noqa: E402 from rsciio.utils.tests import assert_deep_almost_equal # noqa: E402 from rsciio.utils.tools import get_file_handle # noqa: E402 TEST_DATA_PATH = Path(__file__).parent / "data" / "tiff" TEST_NPZ_DATA_PATH = Path(__file__).parent / "data" / "npz" TMP_DIR = tempfile.TemporaryDirectory() def teardown_module(): TMP_DIR.cleanup() def _compare_signal_shape_data(s0, s1): assert s0.data.shape == s1.data.shape np.testing.assert_equal(s0.data, s1.data) def test_rgba16(tmp_path): with zipfile.ZipFile(TEST_DATA_PATH / "test_rgba16.zip", "r") as zipped: zipped.extractall(tmp_path) s = hs.load(tmp_path / "test_rgba16.tif") data = np.load(TEST_NPZ_DATA_PATH / "test_rgba16.npz")["a"] assert (s.data == data).all() assert s.axes_manager.signal_shape == (128, 128) assert s.axes_manager.navigation_shape == (3,) assert s.axes_manager[0].units == t.Undefined assert s.axes_manager[1].units == t.Undefined assert s.axes_manager[2].units == t.Undefined np.testing.assert_allclose(s.axes_manager[0].scale, 1.0, atol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 1.0, atol=1e-5) np.testing.assert_allclose(s.axes_manager[2].scale, 1.0, atol=1e-5) assert s.metadata.General.date == "2014-03-31" assert s.metadata.General.time == "16:35:46" class TestDM3ToTiffConversion: @staticmethod def test_read_unit_um(tmp_path): # Load DM file and save it as tif s = hs.load(TEST_DATA_PATH / "test_dm_image_um_unit.dm3") assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 0.16867, atol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 0.16867, atol=1e-5) assert s.metadata.General.date == "2015-07-20" assert s.metadata.General.time == "18:48:25" fname = tmp_path / "test_export_um_unit.tif" s.save(fname, overwrite=True, export_scale=True) # load tif file s2 = hs.load(fname) assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s2.axes_manager[0].scale, 0.16867, atol=1e-5) np.testing.assert_allclose(s2.axes_manager[1].scale, 0.16867, atol=1e-5) assert s2.metadata.General.date == s.metadata.General.date assert s2.metadata.General.time == s.metadata.General.time assert s2.axes_manager.signal_shape == s.axes_manager.signal_shape assert s2.axes_manager.navigation_shape == s.axes_manager.navigation_shape _compare_signal_shape_data(s, s2) @staticmethod def test_write_read_intensity_axes_DM(): s = hs.load(TEST_DATA_PATH / "test_dm_image_um_unit.dm3") s.metadata.Signal.set_item("quantity", "Electrons (Counts)") d = {"gain_factor": 5.0, "gain_offset": 2.0} s.metadata.Signal.set_item("Noise_properties.Variance_linear_model", d) with tempfile.TemporaryDirectory() as tmpdir: fname = os.path.join(tmpdir, "tiff_files", "test_export_um_unit2.tif") s.save(fname, overwrite=True, export_scale=True) s2 = hs.load(fname) assert_deep_almost_equal( s.metadata.Signal.as_dictionary(), s2.metadata.Signal.as_dictionary() ) class TestLoadingImagesSavedWithImageJ: @staticmethod def test_read_unit_from_imagej(): s = hs.load(TEST_DATA_PATH / "test_loading_image_saved_with_imageJ.tif") assert s.axes_manager.signal_shape == (68, 68) assert s.axes_manager.navigation_shape == () assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 0.16867, atol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 0.16867, atol=1e-5) @staticmethod def test_read_unit_from_imagej_stack(): s = hs.load(TEST_DATA_PATH / "test_loading_image_saved_with_imageJ_stack.tif") assert s.axes_manager.signal_shape == (68, 68) assert s.axes_manager.navigation_shape == (2,) assert s.data.shape == (2, 68, 68) assert s.axes_manager[0].units == t.Undefined assert s.axes_manager[1].units == "µm" assert s.axes_manager[2].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 2.5, atol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 0.16867, atol=1e-5) np.testing.assert_allclose(s.axes_manager[2].scale, 0.16867, atol=1e-5) @staticmethod def test_read_unit_from_imagej_stack_no_scale(): s = hs.load( TEST_DATA_PATH / "test_loading_image_saved_with_imageJ_stack_no_scale.tif" ) assert s.axes_manager.signal_shape == (68, 68) assert s.axes_manager.navigation_shape == (2,) assert s.data.shape == (2, 68, 68) assert s.axes_manager[0].units == t.Undefined assert s.axes_manager[1].units == t.Undefined assert s.axes_manager[2].units == t.Undefined np.testing.assert_allclose(s.axes_manager[0].scale, 1.0, atol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 1.0, atol=1e-5) np.testing.assert_allclose(s.axes_manager[2].scale, 1.0, atol=1e-5) @staticmethod def test_read_unit_from_imagej_no_scale(): s = hs.load( TEST_DATA_PATH / "test_loading_image_saved_with_imageJ_no_scale.tif" ) assert s.axes_manager.signal_shape == (68, 68) assert s.axes_manager.navigation_shape == () assert s.axes_manager[0].units == t.Undefined assert s.axes_manager[1].units == t.Undefined np.testing.assert_allclose(s.axes_manager[0].scale, 1.0, atol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 1.0, atol=1e-5) @staticmethod def test_write_read_unit_imagej(): s = hs.load( TEST_DATA_PATH / "test_loading_image_saved_with_imageJ.tif", convert_units=True, ) s.axes_manager[0].units = "µm" s.axes_manager[1].units = "µm" with tempfile.TemporaryDirectory() as tmpdir: fname2 = os.path.join(tmpdir, "test_loading_image_saved_with_imageJ2.tif") s.save(fname2, export_scale=True, overwrite=True) s2 = hs.load(fname2) assert s2.axes_manager[0].units == "µm" assert s2.axes_manager[1].units == "µm" assert s.data.shape == s2.data.shape assert s2.axes_manager.signal_shape == s.axes_manager.signal_shape assert s2.axes_manager.navigation_shape == s.axes_manager.navigation_shape @staticmethod def test_write_read_unit_imagej_with_description(): s = hs.load(TEST_DATA_PATH / "test_loading_image_saved_with_imageJ.tif") s.axes_manager[0].units = "µm" s.axes_manager[1].units = "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 0.16867, atol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 0.16867, atol=1e-5) with tempfile.TemporaryDirectory() as tmpdir: fname2 = os.path.join(tmpdir, "description.tif") s.save(fname2, export_scale=False, overwrite=True, description="test") s2 = hs.load(fname2) assert s2.axes_manager[0].units == t.Undefined assert s2.axes_manager[1].units == t.Undefined np.testing.assert_allclose(s2.axes_manager[0].scale, 1.0, atol=1e-5) np.testing.assert_allclose(s2.axes_manager[1].scale, 1.0, atol=1e-5) assert s2.axes_manager.signal_shape == s.axes_manager.signal_shape assert s2.axes_manager.navigation_shape == s.axes_manager.navigation_shape fname3 = os.path.join(tmpdir, "description2.tif") s.save(fname3, export_scale=True, overwrite=True, description="test") s3 = hs.load(fname3, convert_units=True) assert s3.axes_manager[0].units == "µm" assert s3.axes_manager[1].units == "µm" np.testing.assert_allclose(s3.axes_manager[0].scale, 0.16867, atol=1e-5) np.testing.assert_allclose(s3.axes_manager[1].scale, 0.16867, atol=1e-5) assert s3.axes_manager.signal_shape == s.axes_manager.signal_shape assert s3.axes_manager.navigation_shape == s.axes_manager.navigation_shape @pytest.mark.parametrize("size", ((50, 50), (2, 50, 50))) def test_lazy_loading(tmp_path, size): dummy_data = np.random.random_sample(size=size) fname = tmp_path / "dummy.tiff" rsciio.tiff.file_writer(fname, {"data": dummy_data}) from_tiff = rsciio.tiff.file_reader(fname, lazy=True) data = from_tiff[0]["data"] fh = get_file_handle(data) # check that the file is open fh.fileno() data = data.compute() np.testing.assert_allclose(data, dummy_data) # After we load to memory, we can close the file manually fh.close() with pytest.raises(ValueError): # file is now closed fh.fileno() def test_lazy_loading_hyperspy_close(tmp_path): # check that the file is closed automatically in hyperspy dummy_data = np.random.random_sample(size=(2, 50, 50)) fname = tmp_path / "dummy.tiff" s = hs.signals.Signal2D(dummy_data) s.save(fname) s2 = hs.load(fname, lazy=True) fh = get_file_handle(s2.data) print("fh", fh) # check that the file is open fh.fileno() s2.compute(close_file=True) np.testing.assert_allclose(s2.data, dummy_data) # when calling compute in hyperspy, # the file should be closed automatically with pytest.raises(ValueError): # file is now closed fh.fileno() class TestLoadingImagesSavedWithDM: @staticmethod @pytest.mark.parametrize("lazy", [True, False]) def test_read_unit_from_DM_stack(tmp_path, lazy): s = hs.load( TEST_DATA_PATH / "test_loading_image_saved_with_DM_stack.tif", lazy=lazy ) assert s.axes_manager.signal_shape == (68, 68) assert s.axes_manager.navigation_shape == (2,) assert s.data.shape == (2, 68, 68) assert s.axes_manager[0].units == "s" assert s.axes_manager[1].units == "µm" assert s.axes_manager[2].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 2.5, atol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 0.16867, atol=1e-5) np.testing.assert_allclose(s.axes_manager[2].scale, 1.68674, atol=1e-5) fname2 = tmp_path / "test_loading_image_saved_with_DM_stack2.tif" s.save(fname2, overwrite=True) s2 = hs.load(fname2) assert s.axes_manager.signal_shape == s2.axes_manager.signal_shape assert s.axes_manager.navigation_shape == s2.axes_manager.navigation_shape _compare_signal_shape_data(s, s2) assert s2.axes_manager[0].units == s.axes_manager[0].units assert s2.axes_manager[1].units == "µm" assert s2.axes_manager[2].units == "µm" np.testing.assert_allclose( s2.axes_manager[0].scale, s.axes_manager[0].scale, atol=1e-5 ) np.testing.assert_allclose( s2.axes_manager[1].scale, s.axes_manager[1].scale, atol=1e-5 ) np.testing.assert_allclose( s2.axes_manager[2].scale, s.axes_manager[2].scale, atol=1e-5 ) np.testing.assert_allclose( s2.axes_manager[0].offset, s.axes_manager[0].offset, atol=1e-5 ) np.testing.assert_allclose( s2.axes_manager[1].offset, s.axes_manager[1].offset, atol=1e-5 ) np.testing.assert_allclose( s2.axes_manager[2].offset, s.axes_manager[2].offset, atol=1e-5 ) if lazy: s.compute() @staticmethod def test_read_unit_from_dm(): fname = TEST_DATA_PATH / "test_loading_image_saved_with_DM.tif" s = hs.load(fname) assert s.axes_manager.signal_shape == (68, 68) assert s.axes_manager.navigation_shape == () assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 0.16867, atol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 0.16867, atol=1e-5) np.testing.assert_allclose(s.axes_manager[0].offset, 139.66264, atol=1e-5) np.testing.assert_allclose(s.axes_manager[1].offset, 128.19276, atol=1e-5) with tempfile.TemporaryDirectory() as tmpdir: fname2 = os.path.join(tmpdir, "DM2.tif") s.save(fname2, overwrite=True) s2 = hs.load(fname2) _compare_signal_shape_data(s, s2) assert s.axes_manager.signal_shape == s2.axes_manager.signal_shape assert s.axes_manager.navigation_shape == s2.axes_manager.navigation_shape assert s2.axes_manager[0].units == "µm" assert s2.axes_manager[1].units == "µm" np.testing.assert_allclose( s2.axes_manager[0].scale, s.axes_manager[0].scale, atol=1e-5 ) np.testing.assert_allclose( s2.axes_manager[1].scale, s.axes_manager[1].scale, atol=1e-5 ) np.testing.assert_allclose( s2.axes_manager[0].offset, s.axes_manager[0].offset, atol=1e-5 ) np.testing.assert_allclose( s2.axes_manager[1].offset, s.axes_manager[1].offset, atol=1e-5 ) class TestSavingTiff: @staticmethod def test_saving_with_custom_tag(): s = hs.signals.Signal2D(np.arange(10 * 15, dtype=np.uint8).reshape((10, 15))) with tempfile.TemporaryDirectory() as tmpdir: fname = os.path.join(tmpdir, "test_saving_with_custom_tag.tif") extratag = [(65000, "s", 1, "Random metadata", False)] s.save(fname, extratags=extratag, overwrite=True) s2 = hs.load(fname) assert s2.original_metadata["Number_65000"] == "Random metadata" def test_write_scale_unit(self): self._test_write_scale_unit(export_scale=True) def test_write_scale_unit_no_export_scale(self): self._test_write_scale_unit(export_scale=False) @staticmethod def _test_write_scale_unit(export_scale=True): """Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct""" s = hs.signals.Signal2D(np.arange(10 * 15, dtype=np.uint8).reshape((10, 15))) s.axes_manager[0].name = "x" s.axes_manager[1].name = "y" s.axes_manager["x"].scale = 0.25 s.axes_manager["y"].scale = 0.25 s.axes_manager["x"].units = "nm" s.axes_manager["y"].units = "nm" with tempfile.TemporaryDirectory() as tmpdir: fname = os.path.join(tmpdir, "test_export_scale_unit_%s.tif" % export_scale) s.save(fname, overwrite=True, export_scale=export_scale) @staticmethod def test_write_scale_unit_not_square_pixel(): """Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct""" s = hs.signals.Signal2D(np.arange(10 * 15, dtype=np.uint8).reshape((10, 15))) s.change_dtype(np.uint8) s.axes_manager[0].name = "x" s.axes_manager[1].name = "y" s.axes_manager["x"].scale = 0.25 s.axes_manager["y"].scale = 0.5 s.axes_manager["x"].units = "nm" s.axes_manager["y"].units = "µm" with tempfile.TemporaryDirectory() as tmpdir: fname = os.path.join(tmpdir, "test_export_scale_unit_not_square_pixel.tif") s.save(fname, overwrite=True, export_scale=True) @staticmethod def test_write_scale_with_undefined_unit(): """Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct""" s = hs.signals.Signal2D(np.arange(10 * 15, dtype=np.uint8).reshape((10, 15))) s.axes_manager[0].name = "x" s.axes_manager[1].name = "y" s.axes_manager["x"].scale = 0.25 s.axes_manager["y"].scale = 0.25 with tempfile.TemporaryDirectory() as tmpdir: fname = os.path.join(tmpdir, "test_export_scale_undefined_unit.tif") s.save(fname, overwrite=True, export_scale=True) @staticmethod def test_write_scale_with_undefined_scale(tmp_path): """Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct""" s = hs.signals.Signal2D(np.arange(10 * 15, dtype=np.uint8).reshape((10, 15))) fname = tmp_path / "test_export_scale_undefined_scale.tif" s.save(fname, overwrite=True, export_scale=True) s1 = hs.load(fname) _compare_signal_shape_data(s, s1) @staticmethod def test_write_scale_with_um_unit(tmp_path): """Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct""" s = hs.load(TEST_DATA_PATH / "test_dm_image_um_unit.dm3") fname = tmp_path / "test_export_um_unit.tif" s.save(fname, overwrite=True, export_scale=True) s1 = hs.load(fname) _compare_signal_shape_data(s, s1) @staticmethod def test_write_scale_unit_image_stack(tmp_path): """Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct""" s = hs.signals.Signal2D( np.arange(5 * 10 * 15, dtype=np.uint8).reshape((5, 10, 15)) ) s.axes_manager[0].scale = 0.25 s.axes_manager[1].scale = 0.5 s.axes_manager[2].scale = 1.5 s.axes_manager[0].units = "nm" s.axes_manager[1].units = "µm" s.axes_manager[2].units = "µm" fname = tmp_path / "test_export_scale_unit_stack2.tif" s.save(fname, overwrite=True, export_scale=True) s1 = hs.load(fname, convert_units=True) _compare_signal_shape_data(s, s1) assert s1.axes_manager[0].units == "pm" # only one unit can be read assert s1.axes_manager[1].units == "µm" assert s1.axes_manager[2].units == "µm" np.testing.assert_allclose(s1.axes_manager[0].scale, 250.0) np.testing.assert_allclose(s1.axes_manager[1].scale, s.axes_manager[1].scale) np.testing.assert_allclose(s1.axes_manager[2].scale, s.axes_manager[2].scale) @staticmethod def test_saving_loading_stack_no_scale(): with tempfile.TemporaryDirectory() as tmpdir: fname = os.path.join(tmpdir, "test_export_scale_unit_stack2.tif") s0 = hs.signals.Signal2D(np.zeros((10, 20, 30))) s0.save(fname, overwrite=True) s1 = hs.load(fname) _compare_signal_shape_data(s0, s1) class TestReadFEIHelios: path = Path(TMP_DIR.name) FEI_Helios_metadata = { "Acquisition_instrument": { "SEM": { "Stage": { "rotation": -2.3611, "tilt": 6.54498e-06, "x": 2.576e-05, "y": -0.000194177, "z": 0.007965, }, "beam_current": 0.00625, "beam_energy": 5.0, "dwell_time": 1e-05, "microscope": 'Helios NanoLab" 660', "working_distance": 4.03466, } }, "General": { "original_filename": "FEI-Helios-Ebeam-8bits.tif", "title": "", "authors": "supervisor", "date": "2016-06-13", "time": "17:06:40", "FileIO": { "0": { "operation": "load", "hyperspy_version": hs.__version__, "io_plugin": "rsciio.tiff", } }, }, "Signal": {"signal_type": ""}, "_HyperSpy": { "Folding": { "original_axes_manager": None, "original_shape": None, "signal_unfolded": False, "unfolded": False, } }, } FEI_navcam_metadata = { "_HyperSpy": { "Folding": { "unfolded": False, "signal_unfolded": False, "original_shape": None, "original_axes_manager": None, } }, "General": { "original_filename": "FEI-Helios-navcam-with-no-IRBeam.tif", "title": "", "date": "2022-05-17", "time": "09:07:08", "authors": "user", "FileIO": {"0": {"operation": "load", "io_plugin": "rsciio.tiff"}}, }, "Signal": {"signal_type": ""}, "Acquisition_instrument": { "SEM": { "Stage": { "x": 0.0699197, "y": 0.000811186, "z": 0, "rotation": 1.07874, "tilt": 6.54498e-06, }, "working_distance": -0.012, "microscope": 'Helios NanoLab" 660', } }, } @classmethod def setup_class(cls): zipf = TEST_DATA_PATH / "tiff_FEI_Helios.zip" with zipfile.ZipFile(zipf, "r") as zipped: zipped.extractall(cls.path) def test_read_FEI_SEM_scale_metadata_8bits(self): fname = self.path / "FEI-Helios-Ebeam-8bits.tif" s = hs.load(fname, convert_units=True) assert s.axes_manager.signal_shape == (512, 471) assert s.axes_manager.navigation_shape == () assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 3.3724, rtol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 3.3724, rtol=1e-5) assert s.data.dtype == "uint8" # delete timestamp from metadata since it's runtime dependent del s.metadata.General.FileIO.Number_0.timestamp self.FEI_Helios_metadata["General"]["original_filename"] = ( "FEI-Helios-Ebeam-8bits.tif" ) assert_deep_almost_equal(s.metadata.as_dictionary(), self.FEI_Helios_metadata) def test_read_FEI_SEM_scale_metadata_16bits(self): fname = self.path / "FEI-Helios-Ebeam-16bits.tif" s = hs.load(fname, convert_units=True) assert s.axes_manager.signal_shape == (512, 471) assert s.axes_manager.navigation_shape == () assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 3.3724, rtol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 3.3724, rtol=1e-5) assert s.data.dtype == "uint16" # delete timestamp from metadata since it's runtime dependent del s.metadata.General.FileIO.Number_0.timestamp self.FEI_Helios_metadata["General"]["original_filename"] = ( "FEI-Helios-Ebeam-16bits.tif" ) assert_deep_almost_equal(s.metadata.as_dictionary(), self.FEI_Helios_metadata) def test_read_FEI_navcam_metadata(self): fname = self.path / "FEI-Helios-navcam.tif" s = hs.load(fname, convert_units=True) assert s.axes_manager.signal_shape == (768, 551) assert s.axes_manager.navigation_shape == () assert s.axes_manager[0].units == "mm" assert s.axes_manager[1].units == "mm" np.testing.assert_allclose(s.axes_manager[0].scale, 0.2640, rtol=0.0001) np.testing.assert_allclose(s.axes_manager[1].scale, 0.2640, rtol=0.0001) assert s.data.dtype == "uint8" # delete timestamp and version from metadata since it's runtime dependent del s.metadata.General.FileIO.Number_0.timestamp del s.metadata.General.FileIO.Number_0.hyperspy_version self.FEI_navcam_metadata["General"]["original_filename"] = ( "FEI-Helios-navcam.tif" ) assert_deep_almost_equal(s.metadata.as_dictionary(), self.FEI_navcam_metadata) def test_read_FEI_navcam_no_IRBeam_metadata(self): fname = self.path / "FEI-Helios-navcam-with-no-IRBeam.tif" s = hs.load(fname, convert_units=True) assert s.axes_manager.signal_shape == (768, 551) assert s.axes_manager.navigation_shape == () assert s.axes_manager[0].units == t.Undefined assert s.axes_manager[1].units == t.Undefined np.testing.assert_allclose(s.axes_manager[0].scale, 1, rtol=0) np.testing.assert_allclose(s.axes_manager[1].scale, 1, rtol=0) assert s.data.dtype == "uint8" # delete timestamp and version from metadata since it's runtime dependent del s.metadata.General.FileIO.Number_0.timestamp del s.metadata.General.FileIO.Number_0.hyperspy_version self.FEI_navcam_metadata["General"]["original_filename"] = ( "FEI-Helios-navcam-with-no-IRBeam.tif" ) assert_deep_almost_equal(s.metadata.as_dictionary(), self.FEI_navcam_metadata) def test_read_FEI_navcam_no_IRBeam_bad_floats_metadata(self): fname = self.path / "FEI-Helios-navcam-with-no-IRBeam-bad-floats.tif" s = hs.load(fname, convert_units=True) assert s.axes_manager.signal_shape == (768, 551) assert s.axes_manager.navigation_shape == () # delete timestamp and version from metadata since it's runtime dependent del s.metadata.General.FileIO.Number_0.timestamp del s.metadata.General.FileIO.Number_0.hyperspy_version self.FEI_navcam_metadata["General"]["original_filename"] = ( "FEI-Helios-navcam-with-no-IRBeam-bad-floats.tif" ) # working distance in the file was a bogus value, # so it shouldn't be in the resulting metadata del self.FEI_navcam_metadata["Acquisition_instrument"]["SEM"][ "working_distance" ] assert_deep_almost_equal(s.metadata.as_dictionary(), self.FEI_navcam_metadata) class TestReadZeissSEM: path = Path(TMP_DIR.name) @classmethod def setup_class(cls): zipf = TEST_DATA_PATH / "tiff_Zeiss_SEM.zip" with zipfile.ZipFile(zipf, "r") as zipped: zipped.extractall(cls.path) def test_read_Zeiss_SEM_scale_metadata_1k_image(self): md = { "Acquisition_instrument": { "SEM": { "Stage": { "rotation": 10.2, "tilt": -0.0, "x": 75.6442, "y": 60.4901, "z": 25.193, }, "Detector": {"detector_type": "HE-SE2"}, "beam_current": 1.0, "beam_energy": 25.0, "dwell_time": 5e-08, "magnification": 105.0, "microscope": "Merlin-61-08", "working_distance": 14.808, } }, "General": { "authors": "LIM", "date": "2015-12-23", "original_filename": "test_tiff_Zeiss_SEM_1k.tif", "time": "09:40:32", "title": "", "FileIO": { "0": { "operation": "load", "hyperspy_version": hs.__version__, "io_plugin": "rsciio.tiff", } }, }, "Signal": {"signal_type": ""}, "_HyperSpy": { "Folding": { "original_axes_manager": None, "original_shape": None, "signal_unfolded": False, "unfolded": False, } }, } fname = self.path / "test_tiff_Zeiss_SEM_1k.tif" s = hs.load(fname, convert_units=True) assert s.axes_manager.signal_shape == (1024, 768) assert s.axes_manager.navigation_shape == () assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 2.614514, rtol=1e-6) np.testing.assert_allclose(s.axes_manager[1].scale, 2.614514, rtol=1e-6) assert s.data.dtype == "uint8" # delete timestamp from metadata since it's runtime dependent del s.metadata.General.FileIO.Number_0.timestamp assert_deep_almost_equal(s.metadata.as_dictionary(), md) def test_read_Zeiss_SEM_scale_metadata_512_image(self): md = { "Acquisition_instrument": { "SEM": { "Stage": { "rotation": 245.8, "tilt": 0.0, "x": 62.9961, "y": 65.3168, "z": 44.678, }, "beam_energy": 5.0, "magnification": "50.00 K X", "microscope": "ULTRA 55-36-06", "working_distance": 3.9, } }, "General": { "authors": "LIBERATO", "date": "2018-09-25", "original_filename": "test_tiff_Zeiss_SEM_512pix.tif", "time": "08:20:42", "title": "", "FileIO": { "0": { "operation": "load", "hyperspy_version": hs.__version__, "io_plugin": "rsciio.tiff", } }, }, "Signal": {"signal_type": ""}, "_HyperSpy": { "Folding": { "original_axes_manager": None, "original_shape": None, "signal_unfolded": False, "unfolded": False, } }, } fname = self.path / "test_tiff_Zeiss_SEM_512pix.tif" s = hs.load(fname, convert_units=True) assert s.axes_manager.signal_shape == (512, 384) assert s.axes_manager.navigation_shape == () assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 0.011649976, rtol=1e-6) np.testing.assert_allclose(s.axes_manager[1].scale, 0.011649976, rtol=1e-6) assert s.data.dtype == "uint8" # delete timestamp from metadata since it's runtime dependent del s.metadata.General.FileIO.Number_0.timestamp assert_deep_almost_equal(s.metadata.as_dictionary(), md) def test_zeiss_multipage_as_separate_signals(self): fname = self.path / "ZEISS_SEM_multipage.tif" s = hs.load(fname, multipage_as_list=True) assert len(s) == 2 assert s[0].axes_manager.signal_shape == (2048, 1536) assert s[0].axes_manager.navigation_shape == () assert s[0].axes_manager.signal_shape == s[1].axes_manager.signal_shape assert s[0].axes_manager.navigation_shape == s[1].axes_manager.navigation_shape assert s[0].metadata.General.time == "22:42:02" assert s[1].metadata.General.time == "22:45:19" assert s[0].original_metadata.CZ_SEM.ap_fib_slice_index == ("Slice Index", 2) assert s[1].original_metadata.CZ_SEM.ap_fib_slice_index == ("Slice Index", 5) # ('C3 Lens I', 716.29, 'mA') # ('C3 Lens I', 716.28, 'mA') np.testing.assert_allclose( s[0].original_metadata.CZ_SEM.ap_c3[1], 716.29, rtol=1e-6 ) np.testing.assert_allclose( s[1].original_metadata.CZ_SEM.ap_c3[1], 716.28, rtol=1e-6 ) np.testing.assert_allclose( s[0].metadata.Acquisition_instrument.SEM.working_distance, 4.5, rtol=1e-3 ) np.testing.assert_allclose( s[1].metadata.Acquisition_instrument.SEM.working_distance, 4.5, rtol=1e-3 ) # yes, working distance is such a low resolution record of beam focus... class TestReadZeissAxioVision: @staticmethod def test_read_RGB_Zeiss_optical_scale_metadata(): s = hs.load(TEST_DATA_PATH / "optical_Zeiss_AxioVision_RGB.tif") assert s.axes_manager.signal_shape == (13, 10) assert s.axes_manager.navigation_shape == () dtype = np.dtype([("R", "u1"), ("G", "u1"), ("B", "u1")]) assert s.data.dtype == dtype assert s.data.shape == (10, 13) assert s.axes_manager[0].units == t.Undefined assert s.axes_manager[1].units == t.Undefined np.testing.assert_allclose(s.axes_manager[0].scale, 1.0, rtol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 1.0, rtol=1e-5) assert s.metadata.General.date == "2016-06-13" assert s.metadata.General.time == "15:59:52" assert s.metadata.General.FileIO.Number_0.hyperspy_version == hs.__version__ assert s.metadata.General.FileIO.Number_0.io_plugin == "rsciio.tiff" @staticmethod def test_read_BW_Zeiss_optical_scale_metadata(): s = hs.load( TEST_DATA_PATH / "optical_Zeiss_AxioVision_BW.tif", force_read_resolution=True, convert_units=True, ) assert s.axes_manager.signal_shape == (13, 10) assert s.axes_manager.navigation_shape == () assert s.data.dtype == np.uint8 assert s.data.shape == (10, 13) assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 169.333, rtol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 169.333, rtol=1e-5) assert s.metadata.General.date == "2016-06-13" assert s.metadata.General.time == "16:08:49" @staticmethod def test_read_BW_Zeiss_optical_scale_metadata_convert_units_false(): s = hs.load( TEST_DATA_PATH / "optical_Zeiss_AxioVision_BW.tif", force_read_resolution=True, convert_units=False, ) assert s.axes_manager.signal_shape == (13, 10) assert s.axes_manager.navigation_shape == () assert s.data.dtype == np.uint8 assert s.data.shape == (10, 13) assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 169.333, rtol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 169.333, rtol=1e-5) @staticmethod def test_read_BW_Zeiss_optical_scale_metadata2(): s = hs.load( TEST_DATA_PATH / "optical_Zeiss_AxioVision_BW.tif", force_read_resolution=True, convert_units=True, ) assert s.axes_manager.signal_shape == (13, 10) assert s.axes_manager.navigation_shape == () assert s.data.dtype == np.uint8 assert s.data.shape == (10, 13) assert s.axes_manager[0].units == "µm" assert s.axes_manager[1].units == "µm" np.testing.assert_allclose(s.axes_manager[0].scale, 169.333, rtol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 169.333, rtol=1e-5) assert s.metadata.General.date == "2016-06-13" assert s.metadata.General.time == "16:08:49" @staticmethod def test_read_BW_Zeiss_optical_scale_metadata3(): s = hs.load( TEST_DATA_PATH / "optical_Zeiss_AxioVision_BW.tif", force_read_resolution=False, ) assert s.axes_manager.signal_shape == (13, 10) assert s.axes_manager.navigation_shape == () assert s.data.dtype == np.uint8 assert s.data.shape == (10, 13) assert s.axes_manager[0].units == t.Undefined assert s.axes_manager[1].units == t.Undefined np.testing.assert_allclose(s.axes_manager[0].scale, 1.0, rtol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 1.0, rtol=1e-5) assert s.metadata.General.date == "2016-06-13" assert s.metadata.General.time == "16:08:49" def test_read_TVIPS_metadata(tmp_path): md = { "Acquisition_instrument": { "TEM": { "Detector": {"Camera": {"exposure": 0.4, "name": "F416"}}, "Stage": { "tilt_alpha": -0.0070000002, "tilt_beta": -0.055, "x": 0.0, "y": -9.2000000506686774e-05, "z": 7.0000001350933871e-06, }, "beam_energy": 99.0, "magnification": 32000.0, } }, "General": { "original_filename": "TVIPS_bin4.tif", "time": "9:01:17", "title": "", "FileIO": { "0": { "operation": "load", "hyperspy_version": hs.__version__, "io_plugin": "rsciio.tiff", } }, }, "Signal": {"signal_type": ""}, "_HyperSpy": { "Folding": { "original_axes_manager": None, "original_shape": None, "signal_unfolded": False, "unfolded": False, } }, } zipf = TEST_DATA_PATH / "TVIPS_bin4.zip" with zipfile.ZipFile(zipf, "r") as zipped: zipped.extractall(tmp_path) s = hs.load(tmp_path / "TVIPS_bin4.tif", convert_units=True) assert s.axes_manager.signal_shape == (1024, 1024) assert s.axes_manager.navigation_shape == () assert s.data.dtype == np.uint8 assert s.data.shape == (1024, 1024) assert s.axes_manager[0].units == "nm" assert s.axes_manager[1].units == "nm" np.testing.assert_allclose(s.axes_manager[0].scale, 1.42080, rtol=1e-5) np.testing.assert_allclose(s.axes_manager[1].scale, 1.42080, rtol=1e-5) # delete timestamp from metadata since it's runtime dependent del s.metadata.General.FileIO.Number_0.timestamp assert_deep_almost_equal(s.metadata.as_dictionary(), md) def test_axes_metadata(): data = np.arange(2 * 5 * 10).reshape((2, 5, 10)) s = hs.signals.Signal2D(data) nav_unit = "s" s.axes_manager.navigation_axes[0].units = nav_unit with tempfile.TemporaryDirectory() as tmpdir: fname = os.path.join(tmpdir, "axes_metadata_default.tif") s.save(fname) s2 = hs.load(fname) assert s2.axes_manager.navigation_axes[0].name == "image series" assert s2.axes_manager.navigation_axes[0].units == nav_unit assert s2.axes_manager.navigation_axes[0].is_binned is False fname2 = os.path.join(tmpdir, "axes_metadata_IYX.tif") s.save(fname2, metadata={"axes": "IYX"}) s3 = hs.load(fname2) assert s3.axes_manager.navigation_axes[0].name == "image series" assert s3.axes_manager.navigation_axes[0].units == nav_unit assert s3.axes_manager.navigation_axes[0].is_binned is False fname2 = os.path.join(tmpdir, "axes_metadata_ZYX.tif") s.save(fname2, metadata={"axes": "ZYX"}) s3 = hs.load(fname2) assert s3.axes_manager.navigation_axes[0].units == nav_unit assert s3.axes_manager.navigation_axes[0].is_binned is False def test_olympus_SIS(): pytest.importorskip("imagecodecs", reason="imagecodecs is required") fname = TEST_DATA_PATH / "olympus_SIS.tif" s = hs.load(fname) # This olympus SIS contains two images: # - the first one is a RGB 8-bits (used for preview purposes) # - the second one is the raw data # only the second one is calibrated. assert len(s) == 2 assert s[0].axes_manager.signal_shape == (112, 101) assert s[0].axes_manager.navigation_shape == () assert s[0].axes_manager.signal_shape == s[1].axes_manager.signal_shape assert s[0].axes_manager.navigation_shape == s[1].axes_manager.navigation_shape am = s[1].axes_manager for axis in am._axes: assert axis.units == "m" np.testing.assert_allclose(axis.scale, 2.3928e-11) np.testing.assert_allclose(axis.offset, 0.0) for ima in s: assert ima.data.shape == (101, 112) assert s[1].data.dtype is np.dtype("uint16") def test_save_angstrom_units(): s = hs.signals.Signal2D(np.arange(200 * 200, dtype="float32").reshape((200, 200))) for axis in s.axes_manager.signal_axes: axis.units = "Å" axis.scale = 0.1 axis.offset = 10 with tempfile.TemporaryDirectory() as tmpdir: fname = os.path.join(tmpdir, "save_angstrom_units.tif") s.save(fname) s2 = hs.load(fname) if Version(tifffile.__version__) >= Version("2020.7.17"): assert s2.axes_manager[0].units == s.axes_manager[0].units assert s2.axes_manager[0].scale == s.axes_manager[0].scale assert s2.axes_manager[0].offset == s.axes_manager[0].offset assert s2.axes_manager[0].is_binned == s.axes_manager[0].is_binned def test_JEOL_SightX(tmp_path): files = [ ("JEOL-SightX-Ronchigram-dummy.tif.gz", 1.0, t.Undefined), ("JEOL-SightX-SAED-dummy.tif.gz", 0.2723, "1 / nm"), ("JEOL-SightX-TEM-mag-dummy.tif.gz", 1.8208, "nm"), ] for file in files: fname = file[0] if fname[-3:] == ".gz": import gzip with gzip.open(TEST_DATA_PATH / fname, "rb") as f: content = f.read() fname = tmp_path / fname[:-3] with open(fname, "wb") as f2: f2.write(content) s = hs.load(fname) else: s = hs.load(TEST_DATA_PATH / file[0]) assert s.axes_manager.signal_shape == (556, 556) assert s.axes_manager.navigation_shape == () for i in range(2): # x, y assert s.axes_manager[i].size == 556 np.testing.assert_allclose(s.axes_manager[i].scale, file[1], rtol=1e-3) assert s.axes_manager[i].units == file[2] class TestReadHamamatsu: path = Path(TMP_DIR.name) @classmethod def setup_class(cls): zipf = TEST_DATA_PATH / "tiff_hamamatsu.zip" with zipfile.ZipFile(zipf, "r") as zipped: zipped.extractall(cls.path) def test_hamamatsu_streak_loadwarnings(self): file = "test_hamamatsu_streak_SCAN.tif" fname = os.path.join(self.path, file) # No hamamatsu_streak_axis_type argument should : # - raise warning # - Initialise uniform data axis with pytest.warns(UserWarning): s = hs.load(fname) assert s.axes_manager.all_uniform # Invalid hamamatsu_streak_axis_type argument should: # - raise warning # - Initialise uniform data axis with pytest.raises(ValueError): _ = hs.load(fname, hamamatsu_streak_axis_type="xxx") s = hs.load(fname, hamamatsu_streak_axis_type="uniform") assert s.axes_manager.all_uniform def test_hamamatsu_streak_scanfile(self): file = "test_hamamatsu_streak_SCAN.tif" fname = os.path.join(self.path, file) with pytest.warns(UserWarning): s = hs.load(fname) assert s.axes_manager.signal_shape == (672, 508) assert s.axes_manager.navigation_shape == () assert s.data.shape == (508, 672) assert s.axes_manager[1].units == "ps" np.testing.assert_allclose(s.axes_manager[1].scale, 2.3081, rtol=1e-3) np.testing.assert_allclose(s.axes_manager[1].offset, 652.3756, rtol=1e-3) np.testing.assert_allclose(s.axes_manager[0].scale, 0.01714, rtol=1e-3) np.testing.assert_allclose(s.axes_manager[0].offset, 231.0909, rtol=1e-3) def test_hamamatsu_streak_focusfile(self): file = "test_hamamatsu_streak_FOCUS.tif" fname = os.path.join(self.path, file) with pytest.warns(UserWarning): s = hs.load(fname) assert s.axes_manager.signal_shape == (672, 508) assert s.axes_manager.navigation_shape == () assert s.data.shape == (508, 672) assert s.axes_manager[1].units == "" np.testing.assert_allclose(s.axes_manager[1].scale, 1.0, rtol=1e-3) np.testing.assert_allclose(s.axes_manager[1].offset, 0.0, rtol=1e-3, atol=1e-5) np.testing.assert_allclose(s.axes_manager[0].scale, 0.01714, rtol=1e-3) np.testing.assert_allclose(s.axes_manager[0].offset, 231.0909, rtol=1e-3) def test_hamamatsu_streak_otherfile(self): # Test case where ScalingXScalingFile="Other" file = "test_hamamatsu_streak_OTHER.tif" fname = os.path.join(self.path, file) with pytest.warns(UserWarning): s = hs.load(fname) assert s.axes_manager.signal_shape == (672, 508) assert s.axes_manager.navigation_shape == () assert s.data.shape == (508, 672) assert s.axes_manager[1].units == "" np.testing.assert_allclose(s.axes_manager[1].scale, 1.0, rtol=1e-3) np.testing.assert_allclose(s.axes_manager[1].offset, 0.0, rtol=1e-3, atol=1e-5) np.testing.assert_allclose(s.axes_manager[0].scale, 1.0, rtol=1e-3) np.testing.assert_allclose(s.axes_manager[0].offset, 0.0, rtol=1e-3, atol=1e-5) def test_hamamatsu_streak_non_uniform_load(self): file = "test_hamamatsu_streak_SCAN.tif" fname = os.path.join(self.path, file) s = hs.load(fname, hamamatsu_streak_axis_type="data") np.testing.assert_allclose( s.original_metadata.ImageDescriptionParsed.Scaling.ScalingYaxis, s.axes_manager[1].axis, rtol=1e-5, ) s = hs.load(fname, hamamatsu_streak_axis_type="functional") np.testing.assert_allclose( s.original_metadata.ImageDescriptionParsed.Scaling.ScalingYaxis, s.axes_manager[1].axis, rtol=1e-5, ) def test_is_hamamatsu_streak(self): file = "test_hamamatsu_streak_SCAN.tif" fname = os.path.join(self.path, file) with pytest.warns(UserWarning): s = hs.load(fname) omd = s.original_metadata.as_dictionary() omd["Artist"] = "TAPTAP" assert not rsciio.tiff._api._is_streak_hamamatsu(omd) _ = omd.pop("Artist") assert not rsciio.tiff._api._is_streak_hamamatsu(omd) omd.update({"Artist": "Copyright Hamamatsu GmbH, 2018"}) omd["Software"] = "TAPTAPTAP" assert not rsciio.tiff._api._is_streak_hamamatsu(omd) _ = omd.pop("Software") assert not rsciio.tiff._api._is_streak_hamamatsu(omd) omd.update({"Software": "HPD-TA 9.5 pf4"}) assert rsciio.tiff._api._is_streak_hamamatsu(omd)